I predict that this thread will either be very short, mirroring the output of the new journal, or will turn into a UD-thread-esque monster complete with LOLcats if the journal proves to be rich new vein of tard. Middle ground highly unlikely. At this point, I'd have to put my money on option one.

Certainly the incestuous little group they have there. I was amused by Axe's reply to Gauger's paper. i mean, why doesn't he just walk a few steps to her desk and ask her his question? It's obviously all for the show, not the substance.

--------------The majority of the stupid is invincible and guaranteed for all time. The terror of their tyranny is alleviated by their lack of consistency. -A. Einstein (H/T, JAD)
If evolution is true, you could not know that it's true because your brain is nothing but chemicals. ?Think about that. -K. Hovind

--------------"But it's disturbing to think someone actually thinks creationism -- having put it's hand on the hot stove every day for the last 400 years -- will get a different result tomorrow." -- midwifetoad

Has anyone else read any of Abel's papers and concluded, like I have, that1. I am astonished at how such nonsense gets past peer review2. question begging shoiuld not be considered a valid scientific endeavor?

Has anyone else read any of Abel's papers and concluded, like I have, that1. I am astonished at how such nonsense gets past peer review2. question begging shoiuld not be considered a valid scientific endeavor?

Not only that, but when i read a paper full of jargon of the author's own creation,

Quote

“Physicodynamics cannot spontaneously traverse The Cybernetic Cut ”

using circular definitions (like CSI and IC: that which cannot be produced by natural causes) , followed by the challenge "prove me wrong! (but I get to make the rules)":

Quote

A single exception of non trivial, unaided spontaneous optimization of formal function by truly natural process would falsify this null hypothesis.

I can only roll my eyes and shrug.

--------------The majority of the stupid is invincible and guaranteed for all time. The terror of their tyranny is alleviated by their lack of consistency. -A. Einstein (H/T, JAD)
If evolution is true, you could not know that it's true because your brain is nothing but chemicals. ?Think about that. -K. Hovind

Anyway, the shiny new ID journal is BIO-Complexity put together by Biologic Institute. The Editorial Board involves the usual suspects (including Gloppy).

All men. Women do the housework, er, copyediting. ;)

That is weird. Why is Gauger isolated like that?

--------------I wouldn't be bothered reading about the selfish gene because it has never been identified. -- Denyse O'Leary, professional moronAgain "how much". I don't think that's a good way to be quantitative.-- gpuccio

32 editors for six articles by a total of 11 authors of which five belong to the editorial team. At the same time five members of the editorial team (underlined) and three authors (Dembski, Meyer, Nelson) are fellows of the Discovery Institute. Quite an endeavor for six articles.

--------------"[...] the type of information we find in living systems is beyond the creative means of purely material processes [...] Who or what is such an ultimate source of information? [...] from a theistic perspective, such an information source would presumably have to be God."

--------------"[...] the type of information we find in living systems is beyond the creative means of purely material processes [...] Who or what is such an ultimate source of information? [...] from a theistic perspective, such an information source would presumably have to be God."

32 editors for six articles by a total of 11 authors of which five belong to the editorial team. At the same time five members of the editorial team (underlined) and three authors (Dembski, Meyer, Nelson) are fellows of the Discovery Institute. Quite an endeavor for six articles.

I predict that this thread will either be very short, mirroring the output of the new journal, or will turn into a UD-thread-esque monster complete with LOLcats if the journal proves to be rich new vein of tard. Middle ground highly unlikely. At this point, I'd have to put my money on option one.

So far, option one is winning big.

--------------...after reviewing the arguments, Iâ€™m inclined to believe that the critics of ENCODEâ€™s bold claim were mostly right, and that the proportion of our genome which is functional is probably between 10 and 20%. --Vincent Torley, uncommondescent.com 1/1/2016

I predict that this thread will either be very short, mirroring the output of the new journal, or will turn into a UD-thread-esque monster complete with LOLcats if the journal proves to be rich new vein of tard. Middle ground highly unlikely. At this point, I'd have to put my money on option one.

The difficulty of explaining evolutionary innovation on a scale that would account for the functional diversity of life and its components continues to dog evolutionary theory. Experiments are shedding light on this, but the complexity of the subject calls for other approaches as well. In particular, computational models that capture some aspects of simple life may provide useful proving grounds for ideas about how evolution can or cannot work. The challenge is to find a model ‘world’ simple enough for rapid simulation but not so simple that the real thing of interest has been lost. That challenge is best met with a model world in which real-world problems can be solved, as otherwise the connection with real innovation would be in doubt. Stylus is a previously described model that meets this criterion by being based on one of the most powerful real-world problem-solving tools: written language. Stylus uses a genetic code to translate gene-like sequences into vector sequences that, when processed according to simple geometric rules, form patterns resembling penned strokes. These translation products, called vector proteins, are functionless unless they form legible Chinese characters, in which case they serve the real function of writing. This coupling of artificial genetic causation to the real world of language makes evolutionary experimentation possible in a context where innovation can have a richness of variety and a depth of causal complexity that at least hints at what is needed to explain the complexity of bacterial proteomes. In order for this possibility to be realized, we here provide a complete Stylus genome as an experimental starting point. To construct it we first wrote a concise description of the Stylus algorithm in Chinese. Using that as a proteome specification, we then constructed the Stylus genes to encode it. In this way the Stylus proteome specifies how its encoding genome is decoded, making it analogous to the gene-expression machinery of bacteria. The complete 70,701 base Stylus genome encodes 223 vector proteins with 112 distinct vector domain types, making it more compact than the smallest bacterial genome but with comparable proteomic complexity for its size.

--------------"[...] the type of information we find in living systems is beyond the creative means of purely material processes [...] Who or what is such an ultimate source of information? [...] from a theistic perspective, such an information source would presumably have to be God."

The difficulty of explaining evolutionary innovation on a scale that would account for the functional diversity of life and its components continues to dog evolutionary theory. Experiments are shedding light on this, but the complexity of the subject calls for other approaches as well. In particular, computational models that capture some aspects of simple life may provide useful proving grounds for ideas about how evolution can or cannot work. The challenge is to find a model ‘world’ simple enough for rapid simulation but not so simple that the real thing of interest has been lost. That challenge is best met with a model world in which real-world problems can be solved, as otherwise the connection with real innovation would be in doubt. Stylus is a previously described model that meets this criterion by being based on one of the most powerful real-world problem-solving tools: written language. Stylus uses a genetic code to translate gene-like sequences into vector sequences that, when processed according to simple geometric rules, form patterns resembling penned strokes. These translation products, called vector proteins, are functionless unless they form legible Chinese characters, in which case they serve the real function of writing. This coupling of artificial genetic causation to the real world of language makes evolutionary experimentation possible in a context where innovation can have a richness of variety and a depth of causal complexity that at least hints at what is needed to explain the complexity of bacterial proteomes. In order for this possibility to be realized, we here provide a complete Stylus genome as an experimental starting point. To construct it we first wrote a concise description of the Stylus algorithm in Chinese. Using that as a proteome specification, we then constructed the Stylus genes to encode it. In this way the Stylus proteome specifies how its encoding genome is decoded, making it analogous to the gene-expression machinery of bacteria. The complete 70,701 base Stylus genome encodes 223 vector proteins with 112 distinct vector domain types, making it more compact than the smallest bacterial genome but with comparable proteomic complexity for its size.

I love how the paper's footer lists the citation as "Vol. 2011, Issue 3". As if there is other content besides this.

Each article in the "Journal of Bio-DougAxe-ity" is its own issue, of course.

--------------"[...] the type of information we find in living systems is beyond the creative means of purely material processes [...] Who or what is such an ultimate source of information? [...] from a theistic perspective, such an information source would presumably have to be God."

The new Ewert, Dembski, Marks article on the Steiner problem didn't change the number of authors who published in Bio-Complexity. The number increased from 11 to 13 when Axe's Stylus paper appeared in 2011. Right now it's still the same 13 authors. 5 of them belong to the Biocomplexity's editorial team of 32 (!) editors. 5 members of the editorial team and 3 authors (Dembski, Meyer, Nelson) are fellows of the Discovery Institute. The 13 authors of the now 7 papers come from only 5 Instituitions:

Marks, Ewert and Montanez seem to prefer the credentials of Baylor rather than their (and Dembski's) other affiliation the Evolutionary Informatics Lab. If they would use the later the number of institutions contributing to the journal would decrease to 4. Taking into account that the Biological Institute belongs to the DI only 3 remain.

--------------"[...] the type of information we find in living systems is beyond the creative means of purely material processes [...] Who or what is such an ultimate source of information? [...] from a theistic perspective, such an information source would presumably have to be God."

It's the usual horse-puckey, I see. Dembski et al. cite me and Jeff Shallit to say that they looked at more genetic algorithms than just stuff like "weasel" that obviously has the target in it. They do this to say that Dave Thomas was wrong in saying:

Quote

They claim that GAs cannot generate true novelty and that all such “answers” are surreptitiously introduced into the program via the algorithm’s fitness testing function

They take issue with a quote Thomas makes, pointing out just how specific that quote was and how general Thomas' claim was.

But one can justify Thomas' claim for Dembski at least, given the following:

Quote

This result refutes the claim that evolutionary algorithms can generate specified complexity, for it means that they can yield specified complexity only if such algorithms along with their fitness functions are carefully adapted to the complex specified targets they are meant to attain. In other words, all the specified complexity we get out of an evolutionary algorithm has first to be put into the construction of the evolutionary algorithm and into the fitness function that guides the algorithm. Evolutionary algorithms therefore do not generate or create specified complexity, but merely harness already existing specified complexity. Like a bump under a rug, the specified complexity problem has been shifted around, but it has not been eliminated.

There are no caveats there about multi-part, complex systems or what-have-you; just a straight-up universal claim about the abilities of evolutionary computation. Given that Dembski hadn't at that point even gotten well onto the dodge of claiming that CSI only meant CSI above his "universal improbability bound", this can only be taken to mean that he intended it to apply even to measures of "local small probability" as discussed in "The Design Inference".

It's the usual horse-puckey, I see. Dembski et al. cite me and Jeff Shallit to say that they looked at more genetic algorithms than just stuff like "weasel" that obviously has the target in it. They do this to say that Dave Thomas was wrong in saying:

Quote

They claim that GAs cannot generate true novelty and that all such “answers” are surreptitiously introduced into the program via the algorithm’s fitness testing function

They take issue with a quote Thomas makes, pointing out just how specific that quote was and how general Thomas' claim was.

But one can justify Thomas' claim for Dembski at least, given the following:

Quote

This result refutes the claim that evolutionary algorithms can generate specified complexity, for it means that they can yield specified complexity only if such algorithms along with their fitness functions are carefully adapted to the complex specified targets they are meant to attain. In other words, all the specified complexity we get out of an evolutionary algorithm has first to be put into the construction of the evolutionary algorithm and into the fitness function that guides the algorithm. Evolutionary algorithms therefore do not generate or create specified complexity, but merely harness already existing specified complexity. Like a bump under a rug, the specified complexity problem has been shifted around, but it has not been eliminated.

There are no caveats there about multi-part, complex systems or what-have-you; just a straight-up universal claim about the abilities of evolutionary computation. Given that Dembski hadn't at that point even gotten well onto the dodge of claiming that CSI only meant CSI above his "universal improbability bound", this can only be taken to mean that he intended it to apply even to measures of "local small probability" as discussed in "The Design Inference".

So how does that work if you are a theistic evolutionist - All living things we see today are the result of evolutionary processes acting on, and from, the first life forms - but none of the specified complexity we see in life today is a result of those processes.

It's the usual horse-puckey, I see. Dembski et al. cite me and Jeff Shallit to say that they looked at more genetic algorithms than just stuff like "weasel" that obviously has the target in it. They do this to say that Dave Thomas was wrong in saying:

Quote

They claim that GAs cannot generate true novelty and that all such “answers” are surreptitiously introduced into the program via the algorithm’s fitness testing function

They take issue with a quote Thomas makes, pointing out just how specific that quote was and how general Thomas' claim was.

But one can justify Thomas' claim for Dembski at least, given the following:

Quote

This result refutes the claim that evolutionary algorithms can generate specified complexity, for it means that they can yield specified complexity only if such algorithms along with their fitness functions are carefully adapted to the complex specified targets they are meant to attain. In other words, all the specified complexity we get out of an evolutionary algorithm has first to be put into the construction of the evolutionary algorithm and into the fitness function that guides the algorithm. Evolutionary algorithms therefore do not generate or create specified complexity, but merely harness already existing specified complexity. Like a bump under a rug, the specified complexity problem has been shifted around, but it has not been eliminated.

There are no caveats there about multi-part, complex systems or what-have-you; just a straight-up universal claim about the abilities of evolutionary computation. Given that Dembski hadn't at that point even gotten well onto the dodge of claiming that CSI only meant CSI above his "universal improbability bound", this can only be taken to mean that he intended it to apply even to measures of "local small probability" as discussed in "The Design Inference".

So how does that work if you are a theistic evolutionist - All living things we see today are the result of evolutionary processes acting on, and from, the first life forms - but none of the specified complexity we see in life today is a result of those processes.

It's the usual horse-puckey, I see. Dembski et al. cite me and Jeff Shallit to say that they looked at more genetic algorithms than just stuff like "weasel" that obviously has the target in it. They do this to say that Dave Thomas was wrong in saying:

Quote

They claim that GAs cannot generate true novelty and that all such “answers” are surreptitiously introduced into the program via the algorithm’s fitness testing function

They take issue with a quote Thomas makes, pointing out just how specific that quote was and how general Thomas' claim was.

But one can justify Thomas' claim for Dembski at least, given the following:

Quote

This result refutes the claim that evolutionary algorithms can generate specified complexity, for it means that they can yield specified complexity only if such algorithms along with their fitness functions are carefully adapted to the complex specified targets they are meant to attain. In other words, all the specified complexity we get out of an evolutionary algorithm has first to be put into the construction of the evolutionary algorithm and into the fitness function that guides the algorithm. Evolutionary algorithms therefore do not generate or create specified complexity, but merely harness already existing specified complexity. Like a bump under a rug, the specified complexity problem has been shifted around, but it has not been eliminated.

There are no caveats there about multi-part, complex systems or what-have-you; just a straight-up universal claim about the abilities of evolutionary computation. Given that Dembski hadn't at that point even gotten well onto the dodge of claiming that CSI only meant CSI above his "universal improbability bound", this can only be taken to mean that he intended it to apply even to measures of "local small probability" as discussed in "The Design Inference".

So how does that work if you are a theistic evolutionist - All living things we see today are the result of evolutionary processes acting on, and from, the first life forms - but none of the specified complexity we see in life today is a result of those processes.

Here, we review what is currently known about the structural components of wood that make these materials so difficult to process industrially and so difficult to degrade biologically. We then move to a more philosophical level by considering whether the existence of lignin and the absence of an organism that can grow on lignin are more readily explained from the Darwinian perspective or from the design perspective.

In the end, it seems plausible that dining on lignin is only difficult, not impossible, but either way the design view seems to offer a more satisfactory account of what we know.

The fatal blow to evolution is already dealt in the abstract:

Quote

The Darwinian account must somehow reconcile 400 million years of failure to evolve a relatively modest innovation—growth on lignin—with a long list of spectacular innovations thought to have evolved in a fraction of that time.

Exactly! And if flight appeared several times, why didn't humans evolve it by now? Because evolution doesn't work and the designer doesn't want us to fly, that's why.

An interview with Matti Leisola in Creation Ministries International here.

Here, we review what is currently known about the structural components of wood that make these materials so difficult to process industrially and so difficult to degrade biologically. We then move to a more philosophical level by considering whether the existence of lignin and the absence of an organism that can grow on lignin are more readily explained from the Darwinian perspective or from the design perspective.

In the end, it seems plausible that dining on lignin is only difficult, not impossible, but either way the design view seems to offer a more satisfactory account of what we know.

The fatal blow to evolution is already dealt in the abstract:

Quote

The Darwinian account must somehow reconcile 400 million years of failure to evolve a relatively modest innovation—growth on lignin—with a long list of spectacular innovations thought to have evolved in a fraction of that time.

Exactly! And if flight appeared several times, why didn't humans evolve it by now? Because evolution doesn't work and the designer doesn't want us to fly, that's why.

An interview with Matti Leisola in Creation Ministries International here.

ETA: My emphasis

I think we should move on to a more philosophical level by considering whether the existence of IDiots is more readily explained from the "Darwinian" perspective or from the design perspective or from the 'some people are just arrogant loons that believe and promote religious bullshit pretending to be science' perspective.

We should also consider, from a more philosophical level of course , that the design account/perspective must somehow reconcile an allegedly perfect, omnipotent, omniscient designer-god creating bullshit believing/promoting IDiots, and that that allegedly perfect god has had at least 13 billion years to get its creation (the universe and everything in it) right and yet it's still far from perfect.

And one more thing we should consider is that the perfect, omnipotent, omniscient designer-god account/perspective must somehow reconcile the thousands of years of the failure of religious beliefs to provide any useful human knowledge, especially in comparison to the fact that reality based science (which also isn't perfect, and has been stifled by religious zealots) has produced an enormous amount of useful knowledge in far less time and continues to produce useful knowledge.

--------------Think not that I am come to send peace on earth: I came not to send peace, but a sword. - Jesus in Matthew 10:34

But those mine enemies, which would not that I should reign over them, bring hither, and slay them before me. -Jesus in Luke 19:27

--------------"But it's disturbing to think someone actually thinks creationism -- having put it's hand on the hot stove every day for the last 400 years -- will get a different result tomorrow." -- midwifetoad

Here, we review what is currently known about the structural components of wood that make these materials so difficult to process industrially and so difficult to degrade biologically. We then move to a more philosophical level by considering whether the existence of lignin and the absence of an organism that can grow on lignin are more readily explained from the Darwinian perspective or from the design perspective.Next, we praise Jesus for the existence of lignin and what it tells us about the poverty of the Darwinian explanation. And finally, we speculate that the long age of Methuselah and other antediluvians listed in Genesis 5 was due to the fact that they were actually made of lignin and thus could live as long as many trees, praise be to God.

Here, we review what is currently known about the structural components of wood that make these materials so difficult to process industrially and so difficult to degrade biologically. We then move to a more philosophical level by considering whether the existence of lignin and the absence of an organism that can grow on lignin are more readily explained from the Darwinian perspective or from the design perspective.

In the end, it seems plausible that dining on lignin is only difficult, not impossible, but either way the design view seems to offer a more satisfactory account of what we know.

The fatal blow to evolution is already dealt in the abstract:

Quote

The Darwinian account must somehow reconcile 400 million years of failure to evolve a relatively modest innovation—growth on lignin—with a long list of spectacular innovations thought to have evolved in a fraction of that time.

Exactly! And if flight appeared several times, why didn't humans evolve it by now? Because evolution doesn't work and the designer doesn't want us to fly, that's why.

An interview with Matti Leisola in Creation Ministries International here.

ETA: My emphasis

I'm not a biochemist, but I think the answer to their riddle can be found in the abstract:

Quote

Fungi accomplish the biodegradation, and the surprising fact that it costs them energy to do so keeps the process gradual.

Bolding mine.

I expect their next paper to argue that extremophiles and the environments they live in are evidence of design because no animals evolved to live there...

Edit to add: I'm not sure why it is surprising that it takes energy to biodegrade lignin

--------------Church burning ebola boy

FTK: I Didn't answer your questions because it beats the hell out of me.

PaV: I suppose for me to be pried away from what I do to focus long and hard on that particular problem would take, quite honestly, hundreds of thousands of dollars to begin to pique my interest.

Here, we review what is currently known about the structural components of wood that make these materials so difficult to process industrially and so difficult to degrade biologically. We then move to a more philosophical level by considering whether the existence of lignin and the absence of an organism that can grow on lignin are more readily explained from the Darwinian perspective or from the design perspective.

In the end, it seems plausible that dining on lignin is only difficult, not impossible, but either way the design view seems to offer a more satisfactory account of what we know.

The fatal blow to evolution is already dealt in the abstract:

Quote

The Darwinian account must somehow reconcile 400 million years of failure to evolve a relatively modest innovation—growth on lignin—with a long list of spectacular innovations thought to have evolved in a fraction of that time.

Exactly! And if flight appeared several times, why didn't humans evolve it by now? Because evolution doesn't work and the designer doesn't want us to fly, that's why.

An interview with Matti Leisola in Creation Ministries International here.

ETA: My emphasis

Because with God, most things are impossible.

Lignin digestion, native radio communication between intelligent brains (why don't we have some sort of ESP?), and getting beyond the limits of evolution.

Evolution, by contrast, has no limits. The IDiots themselves have said so over and over again, and they wouldn't be wrong.

Zachriel has posted two papers about termites merrily digesting lignin on the Uncommonly Dense thread; one was published in 1979.

The lignin thing is just another stupid game from the IDiots anyway. Where does it say that lignin has to be digestible for evolution to be true? Next time they'll probably say that because nothing eats and digests uranium evolution is false.

--------------Think not that I am come to send peace on earth: I came not to send peace, but a sword. - Jesus in Matthew 10:34

But those mine enemies, which would not that I should reign over them, bring hither, and slay them before me. -Jesus in Luke 19:27

Zachriel has posted two papers about termites merrily digesting lignin on the Uncommonly Dense thread; one was published in 1979.

The lignin thing is just another stupid game from the IDiots anyway. Where does it say that lignin has to be digestible for evolution to be true? Next time they'll probably say that because nothing eats and digests uranium evolution is false.

I thought there were extremophiles that use the heat from radioactive decay in lieu of sunlight. Or is it the radiation. I forget.

--------------Any version of ID consistent with all the evidence is indistinguishable from evolution.

Zachriel has posted two papers about termites merrily digesting lignin on the Uncommonly Dense thread; one was published in 1979.

The lignin thing is just another stupid game from the IDiots anyway. Where does it say that lignin has to be digestible for evolution to be true? Next time they'll probably say that because nothing eats and digests uranium evolution is false.

I thought there were extremophiles that use the heat from radioactive decay in lieu of sunlight. Or is it the radiation. I forget.

Zachriel has posted two papers about termites merrily digesting lignin on the Uncommonly Dense thread; one was published in 1979.

The lignin thing is just another stupid game from the IDiots anyway. Where does it say that lignin has to be digestible for evolution to be true? Next time they'll probably say that because nothing eats and digests uranium evolution is false.

I thought there were extremophiles that use the heat from radioactive decay in lieu of sunlight. Or is it the radiation. I forget.

Maybe I missed it but I don't see anything at the end of that link that says anything about anything eating and digesting uranium. I also didn't see anything about extremophiles that use the heat from radioactive decay in lieu of sunlight. What I saw is an article about resistance to radiation. It's interesting but I don't think it refutes what I said.

Besides, it really doesn't matter whether I put uranium or lugnuts in that sentence. What really matters is that the IDiots are playing their usual game where they look for something unrelated to whether evolution (at least in general) occurs and then they try to get people to take them seriously and play along with their ridiculous game.

I'm sure that there are plenty of things that are not digestible and that organisms can't "grow on", yet evolution obviously occurs anyway. For instance, I really don't think that a human can digest and "grow on" water hemlock plants or asteroids but I'm pretty sure that humans have evolved. Even if nothing could eat, digest, or "grow on" lignin, it wouldn't mean a thing to whether evolution occurs.

--------------Think not that I am come to send peace on earth: I came not to send peace, but a sword. - Jesus in Matthew 10:34

But those mine enemies, which would not that I should reign over them, bring hither, and slay them before me. -Jesus in Luke 19:27

Zachriel has posted two papers about termites merrily digesting lignin on the Uncommonly Dense thread; one was published in 1979.

The lignin thing is just another stupid game from the IDiots anyway. Where does it say that lignin has to be digestible for evolution to be true? Next time they'll probably say that because nothing eats and digests uranium evolution is false.

I thought there were extremophiles that use the heat from radioactive decay in lieu of sunlight. Or is it the radiation. I forget.

Maybe I missed it but I don't see anything at the end of that link that says anything about anything eating and digesting uranium. I also didn't see anything about extremophiles that use the heat from radioactive decay in lieu of sunlight. What I saw is an article about resistance to radiation. It's interesting but I don't think it refutes what I said.

Besides, it really doesn't matter whether I put uranium or lugnuts in that sentence. What really matters is that the IDiots are playing their usual game where they look for something unrelated to whether evolution (at least in general) occurs and then they try to get people to take them seriously and play along with their ridiculous game.

I'm sure that there are plenty of things that are not digestible and that organisms can't "grow on", yet evolution obviously occurs anyway. For instance, I really don't think that a human can digest and "grow on" water hemlock plants or asteroids but I'm pretty sure that humans have evolved. Even if nothing could eat, digest, or "grow on" lignin, it wouldn't mean a thing to whether evolution occurs.

I wasn't trying to refute anything you said, I was responding to midwifetoad...

--------------Church burning ebola boy

FTK: I Didn't answer your questions because it beats the hell out of me.

PaV: I suppose for me to be pried away from what I do to focus long and hard on that particular problem would take, quite honestly, hundreds of thousands of dollars to begin to pique my interest.

Feeding is associated with "burning" in animals, but what does feeding mean to an organism that turns radiant energy into complex molecules? Couldn't you say that some organisms feed on energy gradients?

Just asking.

--------------Any version of ID consistent with all the evidence is indistinguishable from evolution.

Feeding is associated with "burning" in animals, but what does feeding mean to an organism that turns radiant energy into complex molecules? Couldn't you say that some organisms feed on energy gradients?

Just asking.

Oh hell yes. Just ask Mike Elzinga... :-)

--------------"But it's disturbing to think someone actually thinks creationism -- having put it's hand on the hot stove every day for the last 400 years -- will get a different result tomorrow." -- midwifetoad

Feeding is associated with "burning" in animals, but what does feeding mean to an organism that turns radiant energy into complex molecules? Couldn't you say that some organisms feed on energy gradients?

Just asking.

I suppose it depends on how "feeding" is defined. In a way it could be said that all organisms "feed" on radiant energy because without radiant energy there wouldn't be any organisms. Feeding is usually thought of as something that's done through a mouth but of course there are many organisms that "feed" on various things in ways other than through a mouth.

A bunch of words could be used to describe the ways that organisms take in the energy they need to survive, such as feed, eat, consume, absorb, drink, digest, inhale, burn, convert, synthesize, and probably more that I can't think of right now. I guess the phrase "Nature will find a way" is true.

By the way, I didn't mean to sound harsh to you or afarensis. That's the trouble with the written word. It leaves a lot to be desired when trying to convey some things.

--------------Think not that I am come to send peace on earth: I came not to send peace, but a sword. - Jesus in Matthew 10:34

But those mine enemies, which would not that I should reign over them, bring hither, and slay them before me. -Jesus in Luke 19:27

Man oh man, are those IDiots screwed up or what? Why on Earth do they think that lignin, or the digestibility of it, or anything else about it, has ANYTHING to do with whether THEIR god or ANY god exists or not?

Something I often think about is that even IF it could be shown that the universe is designed or is likely designed, it would NOT show that the universe was/is designed by the christian god or any other particular god, unless the IDiots can find and show DIRECT evidence to the christian god or some other particular god.

And of course they will never accept that a god other than the christian god is the creator/designer, so any suggestion of a different god is a non-starter with IDiots anyway. Oh sure, they're a so-called "big tent" and they pretend that they're open minded about "the Designer" or "God" or which god is the alleged creator/designer but it's abundantly clear that the only designer/god they believe in and promote is the christian god, and of course they all have their own version of the christian god.

Arguments/assertions that lignin somehow disproves evolution and proves design shows just how desperate, delusional, arrogant, and ridiculous the IDiots are. They KNOW that their beliefs are absolute bullshit and they have no faith in their own so-called faith. They constantly bring up shit that is so absurd, and so irrelevant, and so insane that it's just mind-boggling!

They spend all of their time looking for so-called "gaps" and other even more ridiculous shit and will resort to ANYTHING, no matter how asinine, desperate, or dishonest it is, to try to destroy science and to con people into swallowing their fairy tales. What a way to waste their lives.

And what's next from the IDiot god zombies? No organisms have evolved that eat black holes dipped in galactic quasar sauce with atomic sprinkles on top, therefor jesus?

--------------Think not that I am come to send peace on earth: I came not to send peace, but a sword. - Jesus in Matthew 10:34

But those mine enemies, which would not that I should reign over them, bring hither, and slay them before me. -Jesus in Luke 19:27

--------------"[...] the type of information we find in living systems is beyond the creative means of purely material processes [...] Who or what is such an ultimate source of information? [...] from a theistic perspective, such an information source would presumably have to be God."

These translation products, called vector proteins, are functionless unless they form legible Chinese characters, in which case they serve the real function of writing. This coupling of artificial genetic causation to the real world of language makes evolutionary experimentation possible in a context where innovation can have a richness of variety and a depth of causal complexity that at least hints at what is needed to explain the complexity of bacterial proteomes. In order for this possibility to be realized, we here provide a complete Stylus genome as an experimental starting point.

Kinda goofy, but they built a 70,000 word genome. Not a small amount of work. This was done and written up by May 2011. And then, did they try to 'evolve' it?

Guesses:1) They did, it works, shhh....2) DI gets into a fight: providing a fitness landscape is "smuggling information" in even though that is exactly what the environment does in evolution, crap our analogy defeats our point...shh3) The Chinese speaker bailed 4) The bug evolved into the prolific writings of VJTorley, translated and dumped onto UD for us.

The parts in Avida are the individual steps in the process. If any of the steps in the process are missing, Avida will fail to calculate the EQU function. In this sense Pennock is correct, but we will discuss whether he is correct with respect to the other terms of Behe’s definition.

Isn't the EQU function the irreducibly complex system, and Avida just the environment in which it dwells?

Ewert 2014: The largest model considered here, Avida, uses approximately fifty million digital organisms [14]. The smallest model considered, Sadedin’s geometric model, uses fifty thousand digital organisms [17]. The individual components should be improbable enough that the average guessing time exceeds these numbers. We can determine this probability by taking one over the cube root of the number of digital organisms in the model. We are taking the cube root because we are assuming the minimal number of parts to be three. The actual system may have more parts, but we are interested in the level of complexity that would make it impossible to produce any system of several parts. Making this calculation gives us minimal required levels for complexity of approximately 1/368 for Avida and 1/37 for Sadedin’s model.

If you want to know the probability of calculating the random assembly of a specific sequence of three with an alphabet of 26, it is 1/(26^3) = 1/17576.

If there is a population of random sequences of 50 million, then it is virtually certain to occur. However, if the specific sequence has a length of nineteen, then the probability is 1/(26^19) = 1/7e26, which is virtually impossible in 50 million trials, or even 50 million trials a million million times.

-xposted from uncommon thread

--------------Proudly banned threefour five times by Uncommon Descent.There is only one Tard. The Tard is One.

Ewert 2014: The largest model considered here, Avida, uses approximately fifty million digital organisms [14]. The smallest model considered, Sadedin’s geometric model, uses fifty thousand digital organisms [17]. The individual components should be improbable enough that the average guessing time exceeds these numbers. We can determine this probability by taking one over the cube root of the number of digital organisms in the model. We are taking the cube root because we are assuming the minimal number of parts to be three. The actual system may have more parts, but we are interested in the level of complexity that would make it impossible to produce any system of several parts. Making this calculation gives us minimal required levels for complexity of approximately 1/368 for Avida and 1/37 for Sadedin’s model.

If you want to know the probability of calculating the random assembly of a specific sequence of three with an alphabet of 26, it is 1/(26^3) = 1/17576.

If there is a population of random sequences of 50 million, then it is virtually certain to occur. However, if the specific sequence has a length of nineteen, then the probability is 1/(26^19) = 1/7e26, which is virtually impossible in 50 million trials, or even 50 million trials a million million times.

Ewert 2014: The largest model considered here, Avida, uses approximately fifty million digital organisms [14]. The smallest model considered, Sadedin’s geometric model, uses fifty thousand digital organisms [17]. The individual components should be improbable enough that the average guessing time exceeds these numbers. We can determine this probability by taking one over the cube root of the number of digital organisms in the model. We are taking the cube root because we are assuming the minimal number of parts to be three. The actual system may have more parts, but we are interested in the level of complexity that would make it impossible to produce any system of several parts. Making this calculation gives us minimal required levels for complexity of approximately 1/368 for Avida and 1/37 for Sadedin’s model.

If you want to know the probability of calculating the random assembly of a specific sequence of three with an alphabet of 26, it is 1/(26^3) = 1/17576.

If there is a population of random sequences of 50 million, then it is virtually certain to occur. However, if the specific sequence has a length of nineteen, then the probability is 1/(26^19) = 1/7e26, which is virtually impossible in 50 million trials, or even 50 million trials a million million times.

--------------"[...] the type of information we find in living systems is beyond the creative means of purely material processes [...] Who or what is such an ultimate source of information? [...] from a theistic perspective, such an information source would presumably have to be God."

--------------"[...] the type of information we find in living systems is beyond the creative means of purely material processes [...] Who or what is such an ultimate source of information? [...] from a theistic perspective, such an information source would presumably have to be God."

I see Bio-Complexity has posted their 3rd! (review) article of 2014, by David Snoke. As in "Behe and Snoke." Champagne corks popping!!!!

What is odd to me is that it seemed to get 0 fanfare, from UD, DI news, ENV.... at least that I saw or can find by google.

True, the subject is genuinely embarrassing: "Systems Biology as a Research Program for Intelligent Design." Snoke went to a conference that featured Systems Biology, declares it springs from ID.

But why the silence?

Quote

..in 2001 I wrote:A theory of design can in principle be predictive andquantitative. For example, a computer chip manufacturer,which takes apart a chip made by a rivalcompany, proceeds on the assumption that the circuitsare well designed; this does not lead them toend their investigation, but rather, drives their studyof the chip. The good-design assumption leads tospecific predictions and applications, e.g., the predictionthat it is unlikely to find wires which take upmetal and space but serve no purpose, so that thereshould be few wires which are dead ends, with theapplication that studying any particular wire is likelyto be useful. A bad-design assumption (e.g. that thechip maker made many random circuits and thenjust picked out the ones that worked) would givevery different predictions.

Hmm.... so "bad design" isn't a religious statement. The ID design inference is, and has been, to good design only.

Lots of "there is no junk" and the that the language "design or function or mechanism"="Designed Functions and God's Machines."

How many papers did Bio-Complexity manage to publish this year? A grand total of four! Why, that's 1/8th of a paper per member of the editorial team. By any measure, this is simply astounding productivity. They can be proud of how much they have added to the world's knowledge!

Looking a little deeper, we see that of these four, only one is labeled as a "research article". Two are "critical reviews" and one is a "critical focus". And of these four stellar contributions, one has 2 out of the 3 authors on the editorial team, two are written by members of the editorial team, leaving only one contribution having no one on the editorial team. And that one is written by Winston Ewert, who is a "senior researcher" at Robert J. Marks II's "evolutionary informatics lab". In other words, with all the ideas that ID supporters are brimming with, they couldn't manage to publish a single article by anyone not on the editorial team or directly associated with the editors.

--------------"[...] the type of information we find in living systems is beyond the creative means of purely material processes [...] Who or what is such an ultimate source of information? [...] from a theistic perspective, such an information source would presumably have to be God."

Here we are, 2/3 of the way through 2015, and Biocomplexity has an outstanding -0- publications.

30 or so editors, the work of the full-time research staff of the Biologic institute.......

But as of June they do have a new editor in chief. I'm not sure who should be more embarrassed - us for not noticing, or them for being so irrelevant that nobody noticed, not us and not UD either.

I wonder if Editor Marks will bring back his "Galapagos Finch" character he used to post as on UD. Â That would make their phony science rag almost worth reading. Â Almost. Â

--------------"Science is what got us to the humble place weâ€™re at, and what hard-won progress we might realize comes from science, with ID completely flaccid, religious apologetics bitching from the sidelines." - Eigenstate at UD

Here we are, 2/3 of the way through 2015, and Biocomplexity has an outstanding -0- publications.

30 or so editors, the work of the full-time research staff of the Biologic institute.......

But as of June they do have a new editor in chief. I'm not sure who should be more embarrassed - us for not noticing, or them for being so irrelevant that nobody noticed, not us and not UD either.

Hmm, there have been no publications in 'Bio-Complexity' this year, including since Marks became editor-in-chief, so what is editor-in-chief Marks chiefly editing? And what was the former editor-in-chief chiefly editing?

--------------Think not that I am come to send peace on earth: I came not to send peace, but a sword. - Jesus in Matthew 10:34

But those mine enemies, which would not that I should reign over them, bring hither, and slay them before me. -Jesus in Luke 19:27

Perhaps the only submissions that they're getting are covered by Mr Arrington's assertion that "Some Things are Really Simple"

Indeed why publish if the subject is obviously and indubitably self evident? There is undoubtedly a 100% surety that any superfluous tautologically redundant pleonasms that the ID crowd are fond of would just be sesquipedalian obscurantism. No wonder they don't publish they have nothing to say!

Perhaps the only submissions that they're getting are covered by Mr Arrington's assertion that "Some Things are Really Simple"

Indeed why publish if the subject is obviously and indubitably self evident? There is undoubtedly a 100% surety that any superfluous tautologically redundant pleonasms that the ID crowd are fond of would just be sesquipedalian obscurantism. No wonder they don't publish they have nothing to say!

Just checked BIO-Complexity, the Discovery Institute's peer-reviewed journal, to see if they have published anything this year (they haven't, but it is only November). I did notice though that the last paper they published last year - Reeves/Gauger/Axe on enzymes - is listed with a citation of "BIO-Complexity 2014 (4):1âˆ’16". This struck me as rather odd since BIO-Complexity only published four papers last year in total.

A few moments of digging uncovered that BIO-Complexity is indeed publishing each article as a separate issue, even when they're just 6 pages long and published less than a week apart.

Is this normal for on-line journals? I haven't seen anything similar elsewhere. Or could it be an attempt to make their output seem greater than it is?

Online journals don't need to have issues, but the software they're using has that model. When a paper is published it's put online straight away rather than bundling it together with others as an issue. But the software is set up to publish papers in issues, rather than as they come, so this way they don't need to fight the system.

--------------It is fun to dip into the various threads to watch cluelessness at work in the hands of the confident exponent. - Soapy Sam (so say we all)

Axe and Gauger "tested these proposals by observing how the endpoint of simple evolutionary optimization depends on the starting point. Beginning with optimization of protein-like constructs in the Stylus computational model, we compared promiscuous and junk starting points, where design elements specific to the test function were completely absent, to a starting point that retained most elements of a good design (mutation having disrupted some). In all three cases, evolutionary optimization improved activities by a large factor."

Another round of Â Axe and Gauger running experiments designed to fail, therefore design (except again, some worked, but you know, still design. Not evolution. Nope. Not ever).

Oopsy.

Much handwaving BS follows. Mostly that good 'designs' (defined by them as starting points closer to their target) perform better in a few rounds of directed evolution than more distant starting points, which they call promiscuous or junk (which are totes not-designed, cuz please they be evolutionary random 'junk'). Duh.

My favorite junky 'non-design' is a totally deranged protein* with a huge deletion which apparently fails to achieve full activity in a couple rounds of kit mutagenesis. This kit in my hands only changes a few bases per clone. No insertions more than a base. They don't try shuffling to mimic recombination. Shockingly, it didn't work!! But nearer starting points (again, called designs) do, therefore design and Jesus and all that.

*Their words: "In addition to the 36 residues that are missing in the deletion mutant, another 29 residues are unequivocally prevented from adopting the wild-type conformation because of the missing segment, meaning that the structural disruption extends to 65 residues. Because this is the minimum extent of impact to the whole structure, the images on the right show the maximum amount of wild-type structure that could remain in TEMÎ”. What actually remains may be much less. In addition to the deletion, TEMÎ” carries 32 amino acid substitutions (see Supplement S1 [28])"

When you read that, remember that TEM is ~280 amino acids.

eta: I'm actually most bothered by their misrepresentation of some very fine science.

eta 2: I wonder what the DI and UD say about this paper. Wonder if even they are a bit ashamed.

Life as the managing editor of Bio-Complexity sucks when after having to have to write the journal's sole 2016 article yourself you realize that it's hardly sufficient for more than a single page and that blowing up the figures results in less than 3.5 pages from which 0.5 are used for the title, authors names and affiliation.

Edited by sparc on Sep. 11 2016,22:58

--------------"[...] the type of information we find in living systems is beyond the creative means of purely material processes [...] Who or what is such an ultimate source of information? [...] from a theistic perspective, such an information source would presumably have to be God."

Life as the managing editor of Bio-Complexity sucks when after having to have to write the journal's sole 2016 article yourself you realize that it's hardly sufficient for more than a single page and that blowing up the figures results in less than 3.5 pages from which 0.5 are used for the title, authors names and affiliation.

Since when does a user guide for a piece of software qualify as a scientific paper?

Life as the managing editor of Bio-Complexity sucks when after having to have to write the journal's sole 2016 article yourself you realize that it's hardly sufficient for more than a single page and that blowing up the figures results in less than 3.5 pages from which 0.5 are used for the title, authors names and affiliation.

Since when does a user guide for a piece of software qualify as a scientific paper?

Oh, don't ask that where Gary can hear you.Next thing you know you'll be accused of bashing 'real-science'.

Since they already run a journal by he same name this could have been an opportunity for for the ID-creationists:

Quote

11/22/2016DARPA-BAA-16-08Biological Technologies Office EZ BAABTOThis announcement seeks revolutionary research ideas for topics not being addressed by ongoing BTO programs or other published solicitations. Of particular interest are those proposals from entities (both small and large business) that have never received Government funding, or who do not normally propose to Government solicitations.| Bio-complexity | Bio-systems | Health | Opportunities |

--------------"[...] the type of information we find in living systems is beyond the creative means of purely material processes [...] Who or what is such an ultimate source of information? [...] from a theistic perspective, such an information source would presumably have to be God."

And the original article passed the peer-review of the world-famous ID journal Bio-Complexity. Here's the abstract: Â Â Â Â Â

Quote

Genetic Modeling of Human History Part 1: Comparison of Common Descent and Unique Origin ApproachesOla HÃ¶ssjer, Ann Gauger, Colin Reeves

Abstract

In a series of two papers (Part 1 and 2) we explore what can be said about human history from the DNA variation we observe among us today. Population genetics has been used to infer that we share a common ancestry with apes, that most of our human ancestors emigrated from Africa 50 000 years ago, that they possibly had some mixing with Neanderthals, Denisovans and other archaic populations, and that the early Homo population was never smaller than a few thousand individuals. Population genetics uses mathematical principles for how the genetic composition of a population develops over time through various forces of change, such as mutation, natural selection, genetic drift, recombinations and migration. In this article (Part 1) we investigate the assumptions about this theory and conclude that it is full of gaps and weaknesses. We argue that a unique origin model where humanity arose from one single couple with created diversity seems to explain data at least as well, if not better. We finally propose an alternative simulation approach that could be used in order to val- idate such a model. The mathematical principles of this model are described in more detail in our second paper (Part 2).

All science so far and all emphasis mine.Looking forward for part 2.

ETA: They even discuss if the first couple could have lived in the Middle East.

Edited by sparc on Nov. 08 2016,13:46

--------------"[...] the type of information we find in living systems is beyond the creative means of purely material processes [...] Who or what is such an ultimate source of information? [...] from a theistic perspective, such an information source would presumably have to be God."

Part 2 is actually appeared at the same time (http://bio-complexity.org/ojs.........2016.4).I wonder why their model needs something that they call "created diversity" "for autosomal and X chromosomal DNA" "as a second source of variation"? Is there something special about the Y-chromosome?Looking forward for the next paper which will explain how to dicipher the process of the formation of Eve from Adam's rib out of human genome data.

Edited by sparc on Nov. 08 2016,13:45

--------------"[...] the type of information we find in living systems is beyond the creative means of purely material processes [...] Who or what is such an ultimate source of information? [...] from a theistic perspective, such an information source would presumably have to be God."

And the original article passed the peer-review of the world-famous ID journal Bio-Complexity. Here's the abstract: Â Â Â Â Â Â

Quote

Genetic Modeling of Human History Part 1: Comparison of Common Descent and Unique Origin ApproachesOla HÃ¶ssjer, Ann Gauger, Colin Reeves

Abstract

In a series of two papers (Part 1 and 2) we explore what can be said about human history from the DNA variation we observe among us today. Population genetics has been used to infer that we share a common ancestry with apes, that most of our human ancestors emigrated from Africa 50 000 years ago, that they possibly had some mixing with Neanderthals, Denisovans and other archaic populations, and that the early Homo population was never smaller than a few thousand individuals. Population genetics uses mathematical principles for how the genetic composition of a population develops over time through various forces of change, such as mutation, natural selection, genetic drift, recombinations and migration. In this article (Part 1) we investigate the assumptions about this theory and conclude that it is full of gaps and weaknesses. We argue that a unique origin model where humanity arose from one single couple with created diversity seems to explain data at least as well, if not better. We finally propose an alternative simulation approach that could be used in order to val- idate such a model. The mathematical principles of this model are described in more detail in our second paper (Part 2).

All science so far and all emphasis mine.Looking forward for part 2.

ETA: They even discuss if the first couple could have lived in the Middle East.

ID science at its finest.

1. If Genesis was correct, we would expect to see DNA variation with certain statistical properties in the human population2. But in fact we see completely different statistical properties, incompatible with the account in Genesis.3. Add arbitrary Poof!4. Look again at the DNA variation.5. Repeat 3 and 4 until problem solved.6. Therefore Jesus.

--------------Math is just a language of reality. Its a waste of time to know it. - Robert Byers

There isn't any probability that the letter d is in the word "mathematics"... Â The correct answer would be "not even 0" - JoeG

And the original article passed the peer-review of the world-famous ID journal Bio-Complexity. Here's the abstract: Â Â Â Â Â Â Â

Quote

Genetic Modeling of Human History Part 1: Comparison of Common Descent and Unique Origin ApproachesOla HÃ¶ssjer, Ann Gauger, Colin Reeves

Abstract

In a series of two papers (Part 1 and 2) we explore what can be said about human history from the DNA variation we observe among us today. Population genetics has been used to infer that we share a common ancestry with apes, that most of our human ancestors emigrated from Africa 50 000 years ago, that they possibly had some mixing with Neanderthals, Denisovans and other archaic populations, and that the early Homo population was never smaller than a few thousand individuals. Population genetics uses mathematical principles for how the genetic composition of a population develops over time through various forces of change, such as mutation, natural selection, genetic drift, recombinations and migration. In this article (Part 1) we investigate the assumptions about this theory and conclude that it is full of gaps and weaknesses. We argue that a unique origin model where humanity arose from one single couple with created diversity seems to explain data at least as well, if not better. We finally propose an alternative simulation approach that could be used in order to val- idate such a model. The mathematical principles of this model are described in more detail in our second paper (Part 2).

All science so far and all emphasis mine.Looking forward for part 2.

ETA: They even discuss if the first couple could have lived in the Middle East.

ID science at its finest.

1. Â If Genesis was correct, we would expect to see DNA variation with certain statistical properties in the human population2. Â But in fact we see completely different statistical properties, incompatible with the account in Genesis.3. Â Add arbitrary Poof!4. Â Look again at the DNA variation.5. Â Repeat 3 and 4 until problem solved.6. Â Therefore Jesus.

Since Bio-Complexity's readership remains limited Gauger felt the need to further outline her breathtaking findings in an interview she gave to Salvo which actually lists Science only after Society and Sex in its header.I am afraid though, that not even their sex pages are better than their science section.(original link: http://salvomag.com/new........lap.php)

--------------"[...] the type of information we find in living systems is beyond the creative means of purely material processes [...] Who or what is such an ultimate source of information? [...] from a theistic perspective, such an information source would presumably have to be God."